A variety of approaches have been taken to identify genes and pathways that are associated with traits, such as human disease. In one approach, attempts have been made to use gene expression data to identify genes and pathways associated with such traits. In another approach, genetic information has been used to attempt to identify genes and pathways associated with traits. For instance, clinical measures of a population may be taken to study a trait such as a disease found in the population. Risk factors for the trait can be established from these clinical measures. Demographic and environmental factors are further used to explain variation with respect to the trait. Further, genetic variations associated with traits, such as disease-related traits, as well as the disease itself are used to identify regions in the genome linked to a disease. For example, genetic variations in a population may be used to determine what percentage of the variation of the trait in the population of interest can be explained by genetic variation of a single nucleotide polymorphism (SNP), haplotype, or short tandem repeat (STR) marker. However, as will be described below, the elucidation of genes involved in biological pathways that influence a trait, such as a disease, using either gene expression or genetic expression approaches, is problematic and generally not successful in many instances.